Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
#!/bin/bash
#
# Installation script for GPAW 1.5.2:
# * Using the existing IntelPython3 module on the system which has an optimized
# NumPy and SciPy included.
# * Using the matching version of ase, 3.17.0
# * Compiling with the Intel compilers
#
# The FFT library is discovered at runtime. With the settings used in this script
# this should be MKL FFT, but it is possible to change this at runtime to either
# MKL, FFTW or the built-in NumPy FFT routines, see the installation instructions
# (link below).
#
# The original installation instructions for GPAW can be found at
# https://gitlab.com/gpaw/gpaw/-/blob/1.5.2/doc/install.rst
#
packageID='1.5.2-CentOS8Python3-icc'
install_root=$VSC_SCRATCH/UEABS
systemID=CalcUA-vaughan-rome
download_dir=$install_root/Downloads
install_dir=$install_root/$systemID/Packages/GPAW-manual/$packageID
modules_dir=$install_root/$systemID/Modules/GPAW-manual
build_dir="/dev/shm/$USER/GPAW-manual/$packageID"
libxc_version='4.3.4'
cython_version='0.29.21'
#numpy_version='1.18.5'
numpy_version='1.19.2'
#scipy_version='1.4.2'
scipy_version='1.5.3'
ase_version='3.17.0'
GPAW_version='1.5.2'
GPAWsetups_version='0.9.20000' # Check version on https://wiki.fysik.dtu.dk/gpaw/setups/setups.html
py_maj_min='3.6'
################################################################################
#
# Prepare the system
#
#
# Load modules
#
module purge
module load calcua/2020a
module load intel/2020a
module load buildtools/2020a
module load FFTW/3.3.8-intel-2020a
#
# Create the directories and make sure they are clean if that matters
#
/usr/bin/mkdir -p $download_dir
/usr/bin/mkdir -p $install_dir
/usr/bin/rm -rf $install_dir
/usr/bin/mkdir -p $install_dir
/usr/bin/mkdir -p $modules_dir
/usr/bin/mkdir -p $build_dir
/usr/bin/rm -rf $build_dir
/usr/bin/mkdir -p $build_dir
################################################################################
#
# Download components
#
echo -e "\nDownloading files...\n"
cd $download_dir
# https://gitlab.com/libxc/libxc/-/archive/4.3.4/libxc-4.3.4.tar.bz2
libxc_file="libxc-$libxc_version.tar.bz2"
libxc_url="https://gitlab.com/libxc/libxc/-/archive/$libxc_version"
[[ -f $libxc_file ]] || wget "$libxc_url/$libxc_file"
# We do not download Cython but simply install it using pip.
# NumPy needs customizations, so we need to download and unpack the sources
# https://files.pythonhosted.org/packages/bf/e8/15aea783ea72e2d4e51e3ec365e8dc4a1a32c9e5eb3a6d695b0d58e67cdd/numpy-1.19.2.zip
numpy_file="numpy-$numpy_version.zip"
numpy_url="https://files.pythonhosted.org/packages/bf/e8/15aea783ea72e2d4e51e3ec365e8dc4a1a32c9e5eb3a6d695b0d58e67cdd"
[[ -f $numpy_file ]] || wget "$numpy_url/$numpy_file"
# We do not download ase in this script. As it is pure python and doesn't need
# customization, we will install it using pip right away.
## https://files.pythonhosted.org/packages/d9/08/35969da23b641d3dfca46ba7559f651fcfdca81dbbc00b9058c934e75769/ase-3.17.0.tar.gz
#ase_file="ase-$ase_version.tar.gz"
#ase_url="https://files.pythonhosted.org/packages/d9/08/35969da23b641d3dfca46ba7559f651fcfdca81dbbc00b9058c934e75769"
#[[ -f $ase_file ]] || wget "$ase_url/$ase_file"
# GPAW needs customization, so we need to download and unpack the sources.
# https://files.pythonhosted.org/packages/49/a1/cf54c399f5489cfdda1e8da02cae8bfb4b39d7cb7a895ce86608fcd0e1c9/gpaw-1.5.2.tar.gz
GPAW_file="gpaw-$GPAW_version.tar.gz"
GPAW_url="https://files.pythonhosted.org/packages/49/a1/cf54c399f5489cfdda1e8da02cae8bfb4b39d7cb7a895ce86608fcd0e1c9"
[[ -f $GPAW_file ]] || wget "$GPAW_url/$GPAW_file"
# Download GPAW-setup, a number of setup files for GPAW.
# https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.9.20000.tar.gz
GPAWsetups_file="gpaw-setups-$GPAWsetups_version.tar.gz"
GPAWsetups_url="https://wiki.fysik.dtu.dk/gpaw-files"
[[ -f $GPAWsetups_file ]] || wget "$GPAWsetups_url/$GPAWsetups_file"
################################################################################
#
# Install libxc
#
echo -e "\nInstalling libxc...\n"
cd $build_dir
# Uncompress
tar -xf $download_dir/$libxc_file
cd libxc-$libxc_version
# Configure
autoreconf -i
export CC=icc
#export CFLAGS="-O2 -march=core-avx2 -mtune=core-avx2 -fPIC"
export CFLAGS="-O2 -march=core-avx2 -mtune=core-avx2 -ftz -fp-speculation=safe -fp-model source -fPIC"
#export CFLAGS="-O0 -march=core-avx2 -mtune=core-avx2 -ftz -fp-speculation=safe -fp-model source -fPIC"
./configure --prefix="$install_dir" \
--disable-static --enable-shared --disable-fortran
# Build
make -j 16
# Install
make -j 16 install
# Add bin, lib and include to the PATH variables
PATH=$install_dir/bin:$PATH
LIBRARY_PATH=$install_dir/lib:$LIBRARY_PATH
LD_LIBRARY_PATH=$install_dir/lib:$LD_LIBRARY_PATH
CPATH=$install_dir/include:$CPATH
################################################################################
#
# Install Cython
#
echo -e "\nInstalling Cython...\n"
/usr/bin/mkdir -p "$install_dir/lib/python$py_maj_min/site-packages"
cd $install_dir
/usr/bin/ln -s lib lib64
PYTHONPATH="$install_dir/lib/python$py_maj_min/site-packages"
pip3 install --prefix=$install_dir --no-deps cython==$cython_version
################################################################################
#
# Install NumPy
#
echo -e "\nInstalling NumPy...\n"
cd $build_dir
# Uncompress
unzip $download_dir/$numpy_file
cd numpy-$numpy_version
cat >site.cfg <<EOF
[DEFAULT]
library_dirs = $EBROOTFFTW/lib:$MKLROOT/lib/intel64_lin
include_dirs = $EBROOTFFTW/include:$MKLROOT/include
search_static_first=True
[mkl]
lapack_libs = -Wl:-Bstatic,-Wl:--start-group,mkl_intel_lp64,mkl_intel_thread,mkl_core,-Wl:--end-group,-Wl:-Bdynamic,iomp5
mkl_libs = -Wl:-Bstatic,-Wl:--start-group,mkl_intel_lp64,mkl_intel_thread,mkl_core,-Wl:--end-group,-Wl:-Bdynamic,iomp5
[fftw]
libraries = -Wl:-Bstatic,-Wl:--start-group,fftw3,-Wl:--end-group,-Wl:-Bdynamic
EOF
export CC=icc
export FC=ifort
export CFLAGS="-O2 -march=core-avx2 -mtune=core-avx2 -ftz -fp-speculation=safe -fp-model source -fPIC"
export FFLAGS="-O2 -march=core-avx2 -mtune=core-avx2 -ftz -fp-speculation=safe -fp-model source -fPIC"
python3 setup.py build -j 32 install --prefix $install_dir
# Misses python-dev/python-devel...
################################################################################
#
# Install SciPy
#
echo -e "\nInstalling SciPy...\n"
################################################################################
#
# Install ase
#
echo -e "\nInstalling ase...\n"
pip install --prefix=$install_dir --no-deps ase==$ase_version
################################################################################
#
# Install GPAW-setups
#
echo -e "\nInstalling gpaw-setups...\n"
mkdir -p $install_dir/share/gpaw-setups
cd $install_dir/share/gpaw-setups
tar -xf $download_dir/$GPAWsetups_file --strip-components=1
################################################################################
#
# Install GPAW
#
echo -e "\nInstalling GPAW...\n"
cd $build_dir
# Uncompress
tar -xf $download_dir/$GPAW_file
cd gpaw-$GPAW_version
# Make the customize.py script
mv customize.py customize.py.orig
cat >customize.py <<EOF
print( 'GPAW build INFO: Starting execution of the customization script' )
print( 'GPAW build INFO: Variables at the start of the customization script' )
print( 'GPAW build INFO: libraries = ', libraries )
print( 'GPAW build INFO: mpi_libaries = ', mpi_libraries )
print( 'GPAW build INFO: library_dirs = ', library_dirs )
print( 'GPAW build INFO: mpi_libary_dirs = ', mpi_library_dirs )
print( 'GPAW build INFO: runtime_library_dirs = ', runtime_library_dirs )
print( 'GPAW build INFO: mpi_runtime_libary_dirs = ', mpi_runtime_library_dirs )
print( 'GPAW build INFO: include_dirs = ', include_dirs )
print( 'GPAW build INFO: mpi_include_dirs = ', mpi_include_dirs )
print( 'GPAW build INFO: compiler = ', compiler )
print( 'GPAW build INFO: mpicompiler = ', mpicompiler )
print( 'GPAW build INFO: mpilinker = ', mpilinker )
print( 'GPAW build INFO: extra_compile_args = ', extra_compile_args )
print( 'GPAW build INFO: extra_link_args = ', extra_link_args )
print( 'GPAW build INFO: define_macros = ', define_macros )
print( 'GPAW build INFO: mpi_define_macros = ', mpi_define_macros )
print( 'GPAW build INFO: undef_macros = ', undef_macros )
print( 'GPAW build INFO: scalapack = ', scalapack )
print( 'GPAW build INFO: libvdwxc = ', libvdwxc )
print( 'GPAW build INFO: elpa = ', elpa )
# Reset the lists of libraries as often the wrong BLAS library is picked up.
libraries = []
mpi_libraries = []
# LibXC. Re-add the library (removed by resetting libraries).
# There is no need to add the library directory as we do set library_dirs to the
# content of LIBRARY_PATH further down.
# There should be no need to add the include directory as it is in CPATH which is
# set when we install gpaw.
#include_dirs.append('$install_dir/include')
libraries.append('xc')
# libvdwxc
libvdwxc = False
# ELPA
elpa = False
# ScaLAPACK
scalapack = True
mpi_libraries += ['mkl_scalapack_lp64', 'mkl_blacs_intelmpi_lp64']
mpi_define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
mpi_define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]
# Add EasyBuild LAPACK/BLAS libs
# This should also enable MKL FFTW according to the documentation of GPAW 1.5.2
libraries += ['mkl_intel_lp64', 'mkl_sequential', 'mkl_core']
# Add other EasyBuild library directories.
library_dirs = os.environ['LIBRARY_PATH'].split(':')
# Set the compilers
compiler = os.environ['CC']
mpicompiler = os.environ['MPICC']
mpilinker = os.environ['MPICC']
# We need extra_compile_args to have the right compiler options when re-compiling
# files for gpaw-python. It does imply double compiler options for the other
# compiles though.
extra_compile_args = os.environ['CFLAGS'].split(' ')
print( 'GPAW build INFO: Variables at the end of the customization script' )
print( 'GPAW build INFO: libraries = ', libraries )
print( 'GPAW build INFO: mpi_libaries = ', mpi_libraries )
print( 'GPAW build INFO: library_dirs = ', library_dirs )
print( 'GPAW build INFO: mpi_libary_dirs = ', mpi_library_dirs )
print( 'GPAW build INFO: runtime_library_dirs = ', runtime_library_dirs )
print( 'GPAW build INFO: mpi_runtime_libary_dirs = ', mpi_runtime_library_dirs )
print( 'GPAW build INFO: include_dirs = ', include_dirs )
print( 'GPAW build INFO: mpi_include_dirs = ', mpi_include_dirs )
print( 'GPAW build INFO: compiler = ', compiler )
print( 'GPAW build INFO: mpicompiler = ', mpicompiler )
print( 'GPAW build INFO: mpilinker = ', mpilinker )
print( 'GPAW build INFO: extra_compile_args = ', extra_compile_args )
print( 'GPAW build INFO: extra_link_args = ', extra_link_args )
print( 'GPAW build INFO: define_macros = ', define_macros )
print( 'GPAW build INFO: mpi_define_macros = ', mpi_define_macros )
print( 'GPAW build INFO: undef_macros = ', undef_macros )
print( 'GPAW build INFO: scalapack = ', scalapack )
print( 'GPAW build INFO: libvdwxc = ', libvdwxc )
print( 'GPAW build INFO: elpa = ', elpa )
print( 'GPAW build INFO: Ending execution of the customization script' )
EOF
# Now install gpaw
export CC=icc
export MPICC=mpiicc
export CFLAGS="-O2 -march=core-avx2 -mtune=core-avx2 -qno-openmp-simd"
export CFLAGS="-O2 -march=core-avx2 -mtune=core-avx2 -ftz -fp-speculation=safe -fp-model source -qno-openmp-simd"
export CFLAGS="-O0 -march=core-avx2 -mtune=core-avx2 -ftz -fp-speculation=safe -fp-model source -qno-openmp-simd"
python setup.py install --prefix="$install_dir"
# Easybuild:
# export PYTHONUSERSITE=1
# python setup.py build
# python setup.py install --prefix="$install_dir"
################################################################################
#
# Finish the install
#
echo -e "\nCleaning up and making the LUA-module GPAW-manual/$packageID...\n"
# Go to a different directory before cleaning up the build directory
cd $modules_dir
#/bin/rm -rf $build_dir
# Create a module file
cat >$packageID.lua <<EOF
help([==[
Description
===========
GPAW 1.5.2 for the UEABS benchmark.
Configuration:
* IntelPython3/2020a module, also for NumPy and SciPy
* Parallel GPAW $GPAW_version with ase $ase_version
* FFT library selected at runtime. The default with the path
as set through this module should be MKL but it can be changed
by setting GPAW_FFTWSO as indicated in the install instructions at
https://gitlab.com/gpaw/gpaw/-/blob/$GPAW_version/doc/install.rst
* libxc and GPAW compiled with the Intel compilers
More information
================
- Homepage: http://wiki.fysik.dtu.dk/gpaw
- Documentation:
- GPAW web-based documentation: https://wiki.fysik.dtu.dk/gpaw/
- Version information at https://gitlab.com/gpaw/gpaw/-/blob/$GPAW_version/doc/
- ASE web-based documentation: https://wiki.fysik.dtu.dk/ase/
Included extensions
===================
ase-$ase_version, gpaw-$GPAW_version
]==])
whatis([==[Description: GPAW $GPAW_version with ase $ase_version: UEABS benchmark configuration.]==])
conflict("GPAW")
conflict("GPAW-manual")
if not ( isloaded("calcua/2020a") ) then
load("calcua/2020a")
end
if not ( isloaded("intel/2020a") ) then
load("intel/2020a")
end
if not ( isloaded("IntelPython3/2020a") ) then
load("IntelPython3/2020a")
end
prepend_path("PATH", "$install_dir/bin")
prepend_path("LD_LIBRARY_PATH", "$install_dir/lib")
prepend_path("LIBRARY_PATH", "$install_dir/lib")
prepend_path("PYTHONPATH", "$install_dir/lib/python$py_maj_min/site-packages")
setenv("GPAW_SETUP_PATH", "$install_dir/share/gpaw-setups")
EOF